readme.renumf90
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readme.renumf90 [2012/05/29 11:31] – ignacio | readme.renumf90 [2012/05/29 11:39] – ignacio | ||
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=====Summary===== | =====Summary===== | ||
- | < | + | |
RENUMF90 is a renumbering program for the BLUPF90 family of programs. It | RENUMF90 is a renumbering program for the BLUPF90 family of programs. It | ||
supports multiple traits, different effects per trait, alphanumeric and | supports multiple traits, different effects per trait, alphanumeric and | ||
Line 18: | Line 18: | ||
Warnings | Warnings | ||
- | - input files cannot contain character #. | + | * input files cannot contain character #. |
- | - missing animals have code 0; 00 may be treated as a known animal | + | |
- | Structure of parameter file | + | =====Structure of parameter file====== |
- | =========================== | + | |
The parameter file contains keywords in capital followed by specifications | The parameter file contains keywords in capital followed by specifications | ||
Line 29: | Line 28: | ||
keywords need to occur sequentially, | keywords need to occur sequentially, | ||
- | Bugs | + | |
- | ==== | + | =====Bugs===== |
IDs starting with " | IDs starting with " | ||
- | Fields in the parameter file | + | |
- | ============================= | + | =====Fields in the parameter file===== |
# Parameter file for program renf90; it is translated to parameter | # Parameter file for program renf90; it is translated to parameter | ||
# file for BLUPF90 family of programs. | # file for BLUPF90 family of programs. | ||
- | Lines with # are treated as comments | + | Lines with # are treated as comments |
| | ||
- | + | < | |
DATAFILE | DATAFILE | ||
f1 | f1 | ||
+ | </ | ||
+ | The data file is f1 | ||
- | The data file is f1 | + | <file> |
TRAITS | TRAITS | ||
t1 t2 .. tn | t1 t2 .. tn | ||
+ | </ | ||
+ | t1-tn are positions of traits in datafile; n defines the number of traits | ||
- | t1-tn are positions of traits in datafile; n defines the number of traits | + | < |
- | + | ||
FIELDS_PASSED TO OUTPUT | FIELDS_PASSED TO OUTPUT | ||
p1 p2 .. pm | p1 p2 .. pm | ||
- | + | < | |
- | | + | fields p1-pn are passed to output without changes; can be empty |
+ | < | ||
WEIGHT(S) | WEIGHT(S) | ||
w | w | ||
- | w is position of weight if present; can be empty | + | </ |
- | + | w is position of weight if present; can be empty | |
+ | |||
+ | < | ||
RESIDUAL_VARIANCE | RESIDUAL_VARIANCE | ||
r | r | ||
- | r is matrix of residual (co)variances | + | </ |
+ | r is matrix of residual (co)variances | ||
+ | < | ||
EFFECT | EFFECT | ||
e1.. en type form | e1.. en type form | ||
+ | </ | ||
+ | this line defines one group of effects; e1 .. en are positions of this | ||
+ | effect for all traits; positions can be different for each trait for fixed | ||
+ | effects; for random effects, only one position + 0 (misising) efefct are | ||
+ | possible. | ||
+ | * type is ' | ||
+ | * form is ' | ||
- | this line defines one group of effects; e1 .. en are positions of this | + | < |
- | | + | |
- | | + | |
- | | + | |
- | + | ||
- | type is ' | + | |
- | + | ||
- | form is ' | + | |
NESTED | NESTED | ||
d1 .. dn form | d1 .. dn form | ||
- | + | </ | |
- | | + | optional for covariables only, specifies nesting; form is as above |
| | ||
+ | < | ||
RANDOM | RANDOM | ||
rtype | rtype | ||
+ | </ | ||
+ | |||
+ | the RANDOM keyword occurs only if the current effect is random; | ||
+ | rtype is ' | ||
- | the RANDOM keyword occurs only if the current effect is random; | + | < |
- | rtype is ' | + | |
- | | + | |
OPTIONAL | OPTIONAL | ||
o1 o2.. oq | o1 o2.. oq | ||
+ | < | ||
+ | causes extra effects appended to the animal effect; current options include | ||
+ | ' | ||
+ | permanent environment | ||
- | | + | < |
- | ' | + | |
- | | + | |
- | + | ||
FILE | FILE | ||
fped | fped | ||
+ | </ | ||
- | for animal and sire model only, fped specifies the pedigree file | + | for animal and sire model only, fped specifies the pedigree file |
+ | < | ||
FILE_POS | FILE_POS | ||
an s d alt_dam yob | an s d alt_dam yob | ||
+ | </ | ||
- | for animal effect only; specifies positions in the pedigree file of animal | + | for animal effect only; specifies positions in the pedigree file of animal |
- | | + | an, sire s, dam d, alternate_dam dam rec_dam , and year of birth yob; missing |
- | | + | alt_dam or yob can be replaced by 0; if this line is not given, defaults are |
- | | + | 1 2 3 0 0. If maternal effect is specified, the maternal effect is due to |
- | | + | position of d if alt_dam field is 0, or otherwise is due to alt_dam; If |
- | | + | alt_dam field is not zero, it should include ID of real or recipient |
- | | + | dam. |
+ | < | ||
SNP_FILE | SNP_FILE | ||
fsnp | fsnp | ||
+ | </ | ||
- | optional; fsnp specifies files with ID and SNP information; | + | optional; fsnp specifies files with ID and SNP information; |
- | | + | relationship matrix will be constructed as in Aguilar et al. (2010) and will |
- | | + | include the genomic information; |
- | | + | same format as fped and SNP info needs to start from a fixed column and |
- | | + | include digits 0, 1, 2 and 5; ID and SNP info need to be separated by |
- | | + | at leats one space; see info for program PreGSf90 |
- | + | < | |
PED_DEPTH | PED_DEPTH | ||
p | p | ||
- | + | </ | |
- | | + | |
- | | + | < |
+ | optional for animal effect only; p specifies the depth of pedigree search; | ||
+ | the default is 3; all pedigrees are loaded if p=0. | ||
GEN_INT | GEN_INT |
readme.renumf90.txt · Last modified: 2024/05/22 18:53 by dani